PhysioMotion4D Logo

Getting Started

  • Installation
    • Prerequisites
      • System Requirements
      • Software Dependencies
    • Installation Methods
      • Method 1: Install from PyPI (Recommended)
      • Method 2: Install from Source
    • Optional Dependencies
      • Development Tools
      • Documentation Tools
      • Testing Dependencies
    • Verify Installation
    • Command-Line Tools
    • GPU Setup
      • CUDA Installation
      • PyTorch with CUDA
    • Troubleshooting
      • Common Issues
      • Getting Help
    • Next Steps
  • Quick Start
    • Tutorials
    • Prerequisites
    • Basic Workflow
      • Minimal Slicer-Heart Quickstart
      • Command-Line Interface
      • Python API
    • Step-by-Step Workflow
    • Working with Individual Components
      • Segmentation Only
      • Image Registration Only
      • VTK to USD Conversion
    • Sample Data
      • Download Sample Cardiac CT Data
    • Visualizing Results
      • In NVIDIA Omniverse
      • Using USD Viewer
      • In PyVista
    • Next Steps
    • Common Issues
  • Tutorials
    • Recommended Run Order
    • Tutorial 1: Heart-Gated CT to Animated USD
    • Tutorial 2: CT Segmentation to VTK Surfaces
    • Tutorial 3: Create a PCA Shape Model
    • Tutorial 4: Fit Statistical Model to Patient
    • Tutorial 5: VTK Surface Series to Animated USD
    • Tutorial 6: Reconstruct High-Resolution 4D CT
    • Tutorial 7: DirLab Lung-Lobe PCA Model
    • Tutorial 8: DirLab PCA Time-Series Propagation
    • Tutorial 9: PhysicsNeMo Mesh Stage Model
    • Dataset Notes
  • Examples
    • Complete Workflow Examples
      • Heart-Gated CT Processing
      • Lung 4D-CT Reconstruction
    • Segmentation Examples
      • TotalSegmentator
    • Registration Examples
      • ICON Deep Learning Registration
      • Multi-Phase Cardiac Registration
      • ANTs Multi-Stage Registration
    • USD Conversion Examples
      • VTK Time Series to USD
      • Merge Multiple USD Files
      • Apply Materials to USD
    • Transform and Contour Examples
      • Apply Transform to Images
      • Transform Contours/Meshes
      • Extract Surface from Segmentation
    • Visualization Examples
      • Quick Preview in PyVista
      • Animated Mesh Sequence
    • Batch Processing Examples
      • Process Multiple Patients
      • Parallel Segmentation
    • Data Download Examples
      • Download Slicer-Heart Dataset
    • Custom Workflow Examples
      • Complete Workflow Processing
      • Custom Pipeline with Specific Methods
    • See Also
  • Architecture
    • Data Flow
    • Primary Workflows
    • Component Boundaries
    • CLI Boundary

CLI & Scripts Guide

  • CLI & Scripts Overview
    • How to Use These Resources
    • Target Audience
    • Available Scripts
      • Current Scripts
    • Installation
    • General Workflow
      • Typical Command Structure
      • Output Organization
    • Getting Help
    • Next Steps
  • Heart Gated CT Processing
    • Overview
    • Input Requirements
      • Data Format
      • Image Quality Requirements
    • Basic Usage
      • Single 4D File
      • Multiple 3D Files
      • With Output Directory
    • Command-Line Options
      • Required Arguments
      • Optional Arguments
    • Processing Pipeline
    • Output Files
      • Primary Outputs
      • Intermediate Files
    • Examples
      • Contrast-Enhanced Cardiac CTA
      • Non-Contrast Study with Custom Reference
      • Research Dataset Processing
      • With ANTs Registration
    • Best Practices
      • Choosing Reference Image
      • Performance Optimization
      • Data Quality Tips
    • Troubleshooting
      • Input File Issues
      • Segmentation Quality Issues
      • Registration Failures
      • Memory Issues
    • Expected Processing Time
    • Viewing Results in Omniverse
    • Next Steps
  • Create Statistical Model
    • Overview
    • Installation
    • Quick Start
      • Basic Usage
      • Explicit Sample List
      • With Custom Parameters
    • Command-Line Arguments
      • Required Arguments
      • Optional Arguments
  • Heart Model to Patient Registration
    • Overview
    • Installation
    • Quick Start
      • Basic Usage
      • With PCA Shape Fitting
    • Command-Line Arguments
      • Required Arguments
      • Template Labelmap Configuration
      • PCA Registration Options
      • Registration Configuration
      • Output Options
    • Related Scripts
    • Examples
      • Example 1: Basic Registration
      • Example 2: PCA-Based Registration
    • Output Files
      • Final Results
      • Intermediate Results
    • See Also
  • High-Resolution 4D CT Reconstruction
    • Input Requirements
    • Basic Usage
    • With Upsampling
    • Registration Options
    • Outputs
    • Python API
    • Related Pages
  • VTK to USD Conversion
    • Basic Usage
    • Time Series
    • Appearance Options
    • Splitting
    • Python API
    • Related Pages
  • Best Practices
    • Data Preparation
      • Image Quality Guidelines
      • File Organization
    • Processing Strategies
      • Computational Resources
      • Workflow Optimization
    • Quality Control
      • Verification Checklist
      • Automated Quality Metrics
    • Common Issues and Solutions
      • Poor Segmentation
      • Registration Failure
      • Memory Errors
      • Slow Processing
    • Performance Benchmarks
    • Reproducibility
      • Ensuring Reproducible Results
    • Advanced Topics
      • Custom Reference Selection
      • Multi-Phase Studies
      • Parallel Processing
    • Getting Help
    • Next Steps

API Reference

  • API Reference
    • Base Class
      • Class Reference
        • PhysioMotion4DBase
          • PhysioMotion4DBase.__init__()
          • PhysioMotion4DBase.set_log_level()
          • PhysioMotion4DBase.set_log_classes()
          • PhysioMotion4DBase.set_log_all_classes()
          • PhysioMotion4DBase.get_log_classes()
          • PhysioMotion4DBase.log_debug()
          • PhysioMotion4DBase.log_info()
          • PhysioMotion4DBase.log_warning()
          • PhysioMotion4DBase.log_error()
          • PhysioMotion4DBase.log_critical()
          • PhysioMotion4DBase.log_section()
          • PhysioMotion4DBase.log_progress()
      • Logging
      • Extension Notes
      • See Also
    • Workflow Classes
      • Available Workflows
      • Heart-Gated CT to USD
        • WorkflowConvertHeartGatedCTToUSD
          • WorkflowConvertHeartGatedCTToUSD.__init__()
          • WorkflowConvertHeartGatedCTToUSD.process()
      • CT to VTK
        • WorkflowConvertCTToVTK
          • WorkflowConvertCTToVTK.ANATOMY_GROUPS
          • WorkflowConvertCTToVTK.SEGMENTATION_METHODS
          • WorkflowConvertCTToVTK.__init__()
          • WorkflowConvertCTToVTK.run_workflow()
          • WorkflowConvertCTToVTK.save_surfaces()
          • WorkflowConvertCTToVTK.save_meshes()
          • WorkflowConvertCTToVTK.save_combined_surface()
          • WorkflowConvertCTToVTK.save_combined_mesh()
      • VTK to USD
        • WorkflowConvertVTKToUSD
          • WorkflowConvertVTKToUSD.__init__()
          • WorkflowConvertVTKToUSD.discover_time_series()
          • WorkflowConvertVTKToUSD.run()
      • Statistical Shape Modeling
        • WorkflowCreateStatisticalModel
          • WorkflowCreateStatisticalModel.sample_meshes
          • WorkflowCreateStatisticalModel.reference_mesh
          • WorkflowCreateStatisticalModel.pca_number_of_components
          • WorkflowCreateStatisticalModel.reference_spatial_resolution
          • WorkflowCreateStatisticalModel.reference_buffer_factor
          • WorkflowCreateStatisticalModel.__init__()
          • WorkflowCreateStatisticalModel.set_pca_number_of_components()
          • WorkflowCreateStatisticalModel.run_workflow()
        • WorkflowFitStatisticalModelToPatient
          • WorkflowFitStatisticalModelToPatient.template_model
          • WorkflowFitStatisticalModelToPatient.template_model_surface
          • WorkflowFitStatisticalModelToPatient.template_model_mask
          • WorkflowFitStatisticalModelToPatient.template_model_roi
          • WorkflowFitStatisticalModelToPatient.patient_models
          • WorkflowFitStatisticalModelToPatient.patient_model_surface
          • WorkflowFitStatisticalModelToPatient.combined_patient_model
          • WorkflowFitStatisticalModelToPatient.patient_image
          • WorkflowFitStatisticalModelToPatient.patient_mask
          • WorkflowFitStatisticalModelToPatient.patient_roi
          • WorkflowFitStatisticalModelToPatient.mask_dilation_mm
          • WorkflowFitStatisticalModelToPatient.roi_dilation_mm
          • WorkflowFitStatisticalModelToPatient.transform_tools
          • WorkflowFitStatisticalModelToPatient.registrar_icon
          • WorkflowFitStatisticalModelToPatient.registrar_ants
          • WorkflowFitStatisticalModelToPatient.use_pca_registration
          • WorkflowFitStatisticalModelToPatient.pca_model
          • WorkflowFitStatisticalModelToPatient.pca_number_of_modes
          • WorkflowFitStatisticalModelToPatient.icp_forward_point_transform
          • WorkflowFitStatisticalModelToPatient.icp_inverse_point_transform
          • WorkflowFitStatisticalModelToPatient.icp_template_model_surface
          • WorkflowFitStatisticalModelToPatient.icp_template_model
          • WorkflowFitStatisticalModelToPatient.pca_coefficients
          • WorkflowFitStatisticalModelToPatient.pca_template_model
          • WorkflowFitStatisticalModelToPatient.pca_template_model_surface
          • WorkflowFitStatisticalModelToPatient.m2m_forward_transform
          • WorkflowFitStatisticalModelToPatient.m2m_inverse_transform
          • WorkflowFitStatisticalModelToPatient.m2m_template_model_surface
          • WorkflowFitStatisticalModelToPatient.m2i_forward_transform
          • WorkflowFitStatisticalModelToPatient.m2i_inverse_transform
          • WorkflowFitStatisticalModelToPatient.m2i_template_model_surface
          • WorkflowFitStatisticalModelToPatient.m2i_template_labelmap
          • WorkflowFitStatisticalModelToPatient.registered_template_model
          • WorkflowFitStatisticalModelToPatient.registered_template_model_surface
          • WorkflowFitStatisticalModelToPatient.__init__()
          • WorkflowFitStatisticalModelToPatient.set_mask_dilation_mm()
          • WorkflowFitStatisticalModelToPatient.set_roi_dilation_mm()
          • WorkflowFitStatisticalModelToPatient.set_use_pca_registration()
          • WorkflowFitStatisticalModelToPatient.set_use_mask_to_mask_registration()
          • WorkflowFitStatisticalModelToPatient.set_use_mask_to_image_registration()
          • WorkflowFitStatisticalModelToPatient.register_model_to_model_icp()
          • WorkflowFitStatisticalModelToPatient.register_model_to_model_pca()
          • WorkflowFitStatisticalModelToPatient.register_mask_to_mask()
          • WorkflowFitStatisticalModelToPatient.register_labelmap_to_image()
          • WorkflowFitStatisticalModelToPatient.transform_model()
          • WorkflowFitStatisticalModelToPatient.run_workflow()
      • High-Resolution 4D CT Reconstruction
        • WorkflowReconstructHighres4DCT
          • WorkflowReconstructHighres4DCT.time_series_images
          • WorkflowReconstructHighres4DCT.fixed_image
          • WorkflowReconstructHighres4DCT.reference_frame
          • WorkflowReconstructHighres4DCT.register_reference
          • WorkflowReconstructHighres4DCT.prior_weight
          • WorkflowReconstructHighres4DCT.upsample_to_fixed_resolution
          • WorkflowReconstructHighres4DCT.registration_method
          • WorkflowReconstructHighres4DCT.number_of_iterations
          • WorkflowReconstructHighres4DCT.registrar
          • WorkflowReconstructHighres4DCT.forward_transforms
          • WorkflowReconstructHighres4DCT.inverse_transforms
          • WorkflowReconstructHighres4DCT.losses
          • WorkflowReconstructHighres4DCT.reconstructed_images
          • WorkflowReconstructHighres4DCT.__init__()
          • WorkflowReconstructHighres4DCT.set_number_of_iterations_ants()
          • WorkflowReconstructHighres4DCT.set_number_of_iterations_icon()
          • WorkflowReconstructHighres4DCT.set_prior_weight()
          • WorkflowReconstructHighres4DCT.set_modality()
          • WorkflowReconstructHighres4DCT.set_mask_dilation()
          • WorkflowReconstructHighres4DCT.set_fixed_mask()
          • WorkflowReconstructHighres4DCT.set_moving_masks()
          • WorkflowReconstructHighres4DCT.register_time_series()
          • WorkflowReconstructHighres4DCT.reconstruct_time_series()
          • WorkflowReconstructHighres4DCT.run_workflow()
      • See Also
    • Segmentation Modules
      • Overview
      • Quick Links
      • Choosing a Method
      • Quick Start
        • Basic Segmentation
      • Module Documentation
        • Segmentation Base Class
          • Class Reference
          • Segmentation Contract
          • Anatomy Taxonomy
          • Extending Segmentation
          • See Also
        • TotalSegmentator
          • Class Reference
          • Basic Usage
          • Returned Keys
          • Operational Notes
          • See Also
        • Simpleware Heart Segmenter
          • Class Reference
          • Basic Usage
          • Returned Keys
          • Installation Note
          • See Also
      • Common Operations
        • Structure Extraction
        • Batch Processing
        • Error Handling
      • See Also
    • Image Registration Modules
      • Registration Base Class
        • Class Reference
          • RegisterImagesBase
        • Overview
        • See Also
      • ANTs Registration
        • Class Reference
          • RegisterImagesANTs
        • Basic Registration
        • See Also
      • Greedy Registration
        • Class Reference
          • RegisterImagesGreedy
        • Basic Registration
        • Installation Note
        • See Also
      • ICON Image Registration
        • Class Reference
          • RegisterImagesICON
        • Basic Registration
        • Result Dictionary
        • Configuration
        • See Also
      • Time-Series Registration
        • Class Reference
          • RegisterTimeSeriesImages
        • Basic Usage
        • See Also
      • Common Result Shape
      • Basic Example
      • See Also
    • Model Registration Modules
      • ICP (Iterative Closest Point)
        • Class Reference
          • RegisterModelsICP
      • ICP with ITK Backend
        • Class Reference
          • RegisterModelsICPITK
      • Distance Map Registration
        • Class Reference
          • RegisterModelsDistanceMaps
      • PCA-Based Registration
        • Class Reference
          • RegisterModelsPCA
      • Available Classes
      • Workflow-Level Use
      • See Also
    • USD Generation Modules
      • Overview
      • Quick Links
      • Module Documentation
        • USD Tools
          • Module Reference
        • USD Anatomy Tools
          • Module Reference
        • VTK to USD Conversion
          • Class Reference
        • Low-Level vtk_to_usd Subpackage
          • File Facade
          • Data Structures
          • VTK Readers
          • USD Mesh Conversion
          • Material Manager
          • Mesh Utilities
          • USD Coordinate and Primvar Helpers
          • Primvar Derivations
          • See Also
      • Quick Start
        • Convert VTK to USD
        • Create Anatomical Scene
      • See Also
    • Utility Modules
      • Overview
      • Quick Links
      • Module Documentation
        • Image Tools
          • Module Reference
        • Transform Tools
          • Module Reference
        • Contour Tools
          • Module Reference
        • NRRD Conversion
          • Module Reference
        • Test Tools
          • Module Reference
        • Data Downloads
          • Module Reference
      • See Also
    • CLI Entry-Point API
      • convert_heart_gated_ct_to_usd (CLI)
        • main()
      • convert_ct_to_vtk (CLI)
        • main()
      • convert_vtk_to_usd (CLI)
        • main()
      • create_statistical_model (CLI)
        • main()
      • fit_statistical_model_to_patient (CLI)
        • main()
      • reconstruct_highres_4d_ct (CLI)
        • main()
      • visualize_pca_modes (CLI)
        • main()
      • See Also
    • Quick Navigation
      • By Category
    • Module Index

Developer Guides

  • Architecture Overview
    • Architecture Diagram
    • Workflow Classes
    • Key Boundaries
  • Extending PhysioMotion4D
    • Where to Start
    • Runtime Class Pattern
    • CLI Wrapper Pattern
    • Documentation Requirements
    • Testing Requirements
    • See Also
  • Workflow Development Guide
    • Current Workflow Mapping
    • Workflow Example
    • Adding a Workflow
    • Risk Areas
    • See Also
  • Core Developer Guide
    • Base Class
    • Class Boundaries
    • Validation
    • See Also
  • Segmentation Developer Guide
    • Current Segmentation Contract
    • Implemented Segmenters
    • Adding a New Segmenter
    • Custom Anatomy Looks
    • Development Notes
    • See Also
  • Image Registration Developer Guide
    • Basic Pattern
    • Time Series
    • Development Notes
    • See Also
  • Model Registration Developer Guide
    • Recommended Entry Point
    • Lower-Level Classes
    • Development Notes
    • See Also
  • USD Generation
    • ConvertVTKToUSD
      • Single File
      • Time Series
      • In-Memory Meshes
      • Labeled Meshes with Anatomy Grouping
      • Colormaps
      • Derived Scalars: von Mises Stress
      • Framing Camera
    • Anatomy Materials with USDAnatomyTools
    • Advanced Low-Level Facade
  • Utilities Developer Guide
    • Transform Tools
    • Contour Tools
    • USD Tools
    • USD Anatomy Tools
    • Image Tools
    • See Also

Contributing

  • Contributing
    • Ways to Contribute
    • Getting Started
    • IDE Setup (VS Code / Cursor)
      • Recommended Extensions
      • VS Code Settings
      • Experiment Scripts
      • First-Time Setup Checklist
    • Code Style
      • Formatting and Linting with Ruff
      • Type Checking with mypy
      • Pre-commit Hooks
    • Development Workflow
    • Pull Request Guidelines
    • Testing
      • Write Tests
      • Run Tests
    • Documentation
      • Build Docs Locally
      • Documentation Style
      • Contributing Scripts vs Experiments
      • Docstring Format
    • Code Review Process
      • Review Criteria
    • Reporting Issues
      • Bug Reports
      • Feature Requests
    • Release Process
      • Versioning
      • Making a Release
    • Community Guidelines
    • Getting Help
    • License
    • Acknowledgments
    • See Also
  • Testing
    • Test Categories
    • Specific Areas
    • Real Data and GPU Tests
    • Continuous Integration
    • See Also

Additional Resources

  • FAQ
    • General Questions
      • What is PhysioMotion4D?
      • What data formats are supported?
      • Do I need NVIDIA Omniverse?
    • Installation Questions
      • Do I need a GPU?
      • Which CUDA version is required?
      • What Python version is required?
    • Usage Questions
      • How long does processing take?
      • Which segmentation method should I use?
      • Which registration method should I use?
    • Troubleshooting
    • More Questions?
  • Troubleshooting
    • Installation Issues
      • CUDA Out of Memory
      • CUDA Version Mismatch
      • Import Errors
    • Processing Issues
      • Poor Segmentation Quality
      • Registration Not Converging
    • USD Issues
      • USD Not Animating
      • USD File Too Large
    • Performance Issues
      • Slow Processing
    • Getting Help
  • References
    • Software Citations
    • Related Publications
      • Registration Methods
      • Segmentation Methods
    • Datasets
      • DirLab 4D-CT
      • Slicer-Heart-CT
    • Technologies
      • NVIDIA Omniverse
      • MONAI
      • ITK
    • External Links
    • Contributing
  • Release Notes
    • 2026.05.07 Beta
    • Highlights
PhysioMotion4D
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© Copyright 2026, Stephen R. Aylward, NVIDIA Corporation.

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